Molecular and culture dependent characterization of endolithic bacteria in two beach sand samples and description of Rhizobium endolithicum sp. nov.

Endolithic metagenome analysis of two beach samples collected form Chilika, Odisha, India indicated rich bacterial diversity. While the metagenome analysis of sample one yielded 16S rRNA gene sequences which represent six phyla and 16 genera, sample two yielded very rich diversity representing 17 phyla and 286 genera. Six species of bacteria were isolated from the endolithic enrichments and most of them have 16S rRNA gene sequence similarity of >99 % with known taxa, except for strain JC140(T) having <97 % sequence similarity with taxa with valid names. Strain JC140(T) is Gram-stain-negative and motile. 16S rRNA gene based EzTaxon-e BLAST analysis indicated that strain JC140(T) is closely related with the type strains of Rhizobium yanglingense SH22623(T) (96.8 %), R. alkalisoli CCBAU 01393(T) (96.3 %), R. vignae CCBAU 05176(T) (96.2 %), R. mesosinicum CCBAU 25010(T) (96.1 %) and other members of the genus Rhizobium with <96 % sequence similarity. Strain JC140(T) was characterized based on polyphasic taxonomic analysis. Strain JC140(T) could tolerate up to 5 % salinity, resistant to rifampicin (10 μg) and was positive for catalase and oxidase. The major fatty acid is summed feature 8 (C18:1ω7c/C18:1ω6c) with minor amounts of C19:0 cycloω8c, C16:0, C18:0, C17:0cyclo, summed feature 2 (C14:03OH/C16:1 isoI), summed feature 3 (C16:1ω7c/C16:1ω6c) and 2-hydroxyacid of C15:0. Diphosphatidylglycerol, phosphatidylethanol-amine, phosphatidylcholine, phosphatidylglycerol, unidentified lipids (L1, 2), unidentified phospholipid (PL1-4) constitute the polar lipids of strain JC140(T). The strain has bacteriohopane derivative (BHD2), diplopterol and two unidentified hopanes (UH1, 2) as major hopanoids. Q-10 is the major quinone of strain JC140(T). Based on polyphasic taxonomic analysis, strain JC140(T) represents a species in the genus Rhizobium for which, the name R. endolithicum sp. nov. is proposed. The type strain is JC140(T) (= KCTC32077(T) = CCUG64352(T) = MTCC11723(T) = HAMBI 2447(T)).